20XX | pdb_000020xx

HIV-1 integrase core domain in complex with potent allosteric inhibitors

• PDB DOI: https://doi.org/10.2210/pdb20XX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-12-02 Released: 2025-12-31 
• Deposition Author(s): Nomura, A., Orita, T., Furuzono, T., Adachi, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Discovery and optimization of novel and potent allosteric HIV-1 integrase inhibitors with a spiro[indene] moiety.

Adachi, K., Manabe, T., Yamasaki, T., Suma, A., Ogoshi, Y., Takahashi, A., Orita, T., Nomura, A., Adachi, T., Ohata, Y., Akiyama, Y., Miyazaki, S.

(2026) Bioorg Med Chem 134: 118526-118526

• PubMed: 41429097 
• DOI: https://doi.org/10.1016/j.bmc.2025.118526
• Primary Citation Related Structures: 
  20XX


• PubMed Abstract: 
  

  Allosteric inhibitors of HIV-1 integrase offer a promising approach to block an essential process in HIV-1 replication and offer a new strategy for HIV treatment. During the course of our drug discovery investigations, we identified novel allosteric HIV-1 integrase inhibitor 1 which has a conformationally constrained spiro indane scaffold. Our subsequent medicinal chemistry efforts using a structure-based drug design focused on the efficacies of related compound 5 against not only the wild type enzyme but also enzymes with polymorphisms and resistance mutations. As a result, we identified compound 38 f, which exhibited the desired efficacy against major polymorphisms and resistance mutations (EC ₅₀ (WT) = 0.0040 μM, EC ₅₀ (T124N) = 0.0048 μM, EC ₅₀ (T125A) = 0.0038 μM, EC ₅₀ (A128T) = 0.0057 μM), potent anti-HIV activity in the human serum assay (EC ₅₀ (HS50%) = 0.091 μM), and preferable PK profiles in rats (Cl _tot  = 0.017 L/h/kg, MRT = 12.5 h, BA = 71.4 %).

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Organizational Affiliation: 
• Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan. Electronic address: [e-mail].
Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.37 kDa 
• Atom Count: 1,190 
• Modeled Residue Count: 137 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	166	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1MCX (Subject of Investigation/LOI)	B [auth A]	(2~{S})-2-[(3~{a}~{R},7~{a}~{R})-1'-ethyl-5'-methyl-spiro[1,3,3~{a},4,5,6,7,7~{a}-octahydroindene-2,3'-indene]-4'-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid C26 H36 O3 WKRWRLKEDSHXLQ-PWHSHALESA-N
1PE (Subject of Investigation/LOI)	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 72.03	β = 90
c = 66.34	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Nomura, A., Orita, T., Furuzono, T., Adachi, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Database references